Clay

(credit: Wikimedia Commons)

What is it?

Clay is a minimalistic Clojure tool for data visualization and literate programming, compatible with the Kindly convention.

Also see the Babashka Conf 2023 talk.

Goals

• Easily explore & share things for others to easily pick & use.
• Encourage writing Kindly-compatible notes for future compatiblity with other tools.
• Flow with the REPL: encourage user interactions that flow naturally with the typical use of Clojure in editors and REPLs.

Setup

For rendering documents like this one with Clay, you need to:

• add kindly-default and Clay as dependencies
• call (kindly-default/setup!) and (clay/start!) (see below)

To enjoy Clay's dynamic interaction, you also need to inform it about code evaluations. This requires some setup at the your editor.

See the suggested setup for popular editors below. If your favourite editor is not supported yet, let us talk and make it work.

VSCode Calva

(to be updated soon)

Please add the following command to your keybindings.json file at the VScode setup (you may pick another key, of course). This command would evaluate a piece of code and send the result to be visualized in Clay.

{
"key": "ctrl+shift+enter",
"command": "calva.runCustomREPLCommand",
"args": "(scicloj.clay.v2.api/handle-form! (quote $current-form))"
}

Emacs CIDER

(to be updated soon)

Please load clay.el at your Emacs config.

It offers the following functions, that you may wish to create keybindings for:

Starting a Clay namespace

Now, we can write a namespace and play with Clay.

(ns index
  (:require [scicloj.clay.v2.api :as clay]
            [scicloj.kindly.v3.api :as kindly]
            [scicloj.kindly.v3.kind :as kind]
            [scicloj.kindly-default.v1.api :as kindly-default]))

(defonce memoized-slurp
  (memoize slurp))

nil

Initialize Kindly's default.

(kindly-default/setup!)

:ok

Let us start Clay.

(clay/start!)

(clay/swap-options!
 assoc
 :remote-repo {:git-url "https://github.com/scicloj/clay"
               :branch "main"})

:ok

These initializations can also be done in a user.clj file, making them available for all namespaces in the project. The browser view should open automatically.

A few useful actions

Showing the whole namespace:

(comment
  (clay/show-doc! "notebooks/index.clj"))

Writing the document:

(comment
  (clay/show-doc-and-write-html!
   "notebooks/index.clj"
   {:toc? true}))

Reopening the Clay view in the browser (in case you closed the browser tab previously opened by clay/start!)

(comment
  (clay/browse!))

These can be conveniently bound to functions and keys at your editor (to b documented soon).

Interaction

Clay responds to user evaluations by displaying the result visually.

(+ 1111 2222)

3333

In Emacs CIDER, after evaluation of a form (or a region), the browser view should show the evaluation result. In VSCode Calva, a similar effect can be achieved using the dedicated command and keybinding defined above.

Kinds

The way things should be visualized is determined by the advice of Kindly. In this namespace we demonstrate Kindly's default advice. User-defined Kindly advices should work as well. Kindly advises tools (like Clay) about the kind of way a given context should be displayed, by assigning to it a so-called kind. Please refer to the Kindly documentation for details about specifying and using kinds.

Examples

Plain values

By default, when there is no kind information provided by Kindly, values are pretty-printed.

(def people-as-maps
  (->> (range 29)
       (mapv (fn [i]
               {:preferred-language (["clojure" "clojurescript" "babashka"]
                                     (rand-int 3))
                :age (rand-int 100)}))))

(def people-as-vectors
  (->> people-as-maps
       (mapv (juxt :preferred-language :age))))

people-as-maps

[{:preferred-language "clojurescript", :age 3}
 {:preferred-language "babashka", :age 85}
 {:preferred-language "clojure", :age 43}
 {:preferred-language "clojure", :age 50}
 {:preferred-language "clojure", :age 13}
 {:preferred-language "clojure", :age 47}
 {:preferred-language "babashka", :age 19}
 {:preferred-language "babashka", :age 82}
 {:preferred-language "clojure", :age 86}
 {:preferred-language "babashka", :age 18}
 {:preferred-language "clojure", :age 5}
 {:preferred-language "babashka", :age 70}
 {:preferred-language "clojurescript", :age 75}
 {:preferred-language "clojurescript", :age 12}
 {:preferred-language "clojure", :age 26}
 {:preferred-language "babashka", :age 60}
 {:preferred-language "clojurescript", :age 72}
 {:preferred-language "babashka", :age 66}
 {:preferred-language "clojure", :age 76}
 {:preferred-language "babashka", :age 37}
 {:preferred-language "clojure", :age 46}
 {:preferred-language "clojurescript", :age 75}
 {:preferred-language "babashka", :age 37}
 {:preferred-language "babashka", :age 18}
 {:preferred-language "babashka", :age 75}
 {:preferred-language "babashka", :age 63}
 {:preferred-language "clojurescript", :age 83}
 {:preferred-language "babashka", :age 15}
 {:preferred-language "clojurescript", :age 20}]

people-as-vectors

[["clojurescript" 3]
 ["babashka" 85]
 ["clojure" 43]
 ["clojure" 50]
 ["clojure" 13]
 ["clojure" 47]
 ["babashka" 19]
 ["babashka" 82]
 ["clojure" 86]
 ["babashka" 18]
 ["clojure" 5]
 ["babashka" 70]
 ["clojurescript" 75]
 ["clojurescript" 12]
 ["clojure" 26]
 ["babashka" 60]
 ["clojurescript" 72]
 ["babashka" 66]
 ["clojure" 76]
 ["babashka" 37]
 ["clojure" 46]
 ["clojurescript" 75]
 ["babashka" 37]
 ["babashka" 18]
 ["babashka" 75]
 ["babashka" 63]
 ["clojurescript" 83]
 ["babashka" 15]
 ["clojurescript" 20]]

Pretty printing

With the the :kind/pprint kind, this can behaviour can be made explicit (overriding other inferred kinds if necessary).

(kind/pprint people-as-maps)

[{:preferred-language "clojurescript", :age 3}
 {:preferred-language "babashka", :age 85}
 {:preferred-language "clojure", :age 43}
 {:preferred-language "clojure", :age 50}
 {:preferred-language "clojure", :age 13}
 {:preferred-language "clojure", :age 47}
 {:preferred-language "babashka", :age 19}
 {:preferred-language "babashka", :age 82}
 {:preferred-language "clojure", :age 86}
 {:preferred-language "babashka", :age 18}
 {:preferred-language "clojure", :age 5}
 {:preferred-language "babashka", :age 70}
 {:preferred-language "clojurescript", :age 75}
 {:preferred-language "clojurescript", :age 12}
 {:preferred-language "clojure", :age 26}
 {:preferred-language "babashka", :age 60}
 {:preferred-language "clojurescript", :age 72}
 {:preferred-language "babashka", :age 66}
 {:preferred-language "clojure", :age 76}
 {:preferred-language "babashka", :age 37}
 {:preferred-language "clojure", :age 46}
 {:preferred-language "clojurescript", :age 75}
 {:preferred-language "babashka", :age 37}
 {:preferred-language "babashka", :age 18}
 {:preferred-language "babashka", :age 75}
 {:preferred-language "babashka", :age 63}
 {:preferred-language "clojurescript", :age 83}
 {:preferred-language "babashka", :age 15}
 {:preferred-language "clojurescript", :age 20}]

(kind/pprint people-as-vectors)

[["clojurescript" 3]
 ["babashka" 85]
 ["clojure" 43]
 ["clojure" 50]
 ["clojure" 13]
 ["clojure" 47]
 ["babashka" 19]
 ["babashka" 82]
 ["clojure" 86]
 ["babashka" 18]
 ["clojure" 5]
 ["babashka" 70]
 ["clojurescript" 75]
 ["clojurescript" 12]
 ["clojure" 26]
 ["babashka" 60]
 ["clojurescript" 72]
 ["babashka" 66]
 ["clojure" 76]
 ["babashka" 37]
 ["clojure" 46]
 ["clojurescript" 75]
 ["babashka" 37]
 ["babashka" 18]
 ["babashka" 75]
 ["babashka" 63]
 ["clojurescript" 83]
 ["babashka" 15]
 ["clojurescript" 20]]

Datasets

tech.ml.dataset datasets currently use the default printing of the library, Let us create such a dataset using Tablecloth.

(require '[tablecloth.api :as tc])

nil

(-> {:x (range 6)
     :y [:A :B :C :A :B :C]}
    tc/dataset)

(-> {:x [1 [2 3] 4]
     :y [:A :B :C]}
    tc/dataset)

(-> [{:x 1 :y 2 :z 3}
     {:y 4 :z 5}]
    tc/dataset)

(-> people-as-maps
    tc/dataset)

Tables

The :kind/table kind can be handy for an interactive table view.

(kind/table
 {:column-names [:preferred-language :age]
  :row-vectors people-as-vectors})

(kind/table
 {:column-names [:preferred-language :age]
  :row-maps people-as-maps})

(-> people-as-maps
    tc/dataset
    kind/table)

Hiccup

Hiccup, a popular Clojure way to represent HTML, can be specified by kind:

(kind/hiccup
 [:big [:big [:p {:style ; https://www.htmlcsscolor.com/hex/7F5F3F
                  {:color "#7F5F3F"}}
              "hello"]]])

Images

(import javax.imageio.ImageIO
        java.net.URL)

java.net.URL

(defonce image
  (->  "https://upload.wikimedia.org/wikipedia/commons/2/2c/Clay-ss-2005.jpg"
       (URL.)
       (ImageIO/read)))

nil

image

Vega and Vega-Lite

(defn vega-lite-point-plot [data]
  (-> {:data {:values data},
       :mark "point"
       :encoding
       {:size {:field "w" :type "quantitative"}
        :x {:field "x", :type "quantitative"},
        :y {:field "y", :type "quantitative"},
        :fill {:field "z", :type "nominal"}}}
      kind/vega-lite))

(defn random-data [n]
  (->> (repeatedly n #(- (rand) 0.5))
       (reductions +)
       (map-indexed (fn [x y]
                      {:w (rand-int 9)
                       :z (rand-int 9)
                       :x x
                       :y y}))))

(defn random-vega-lite-plot [n]
  (-> n
      random-data
      vega-lite-point-plot))

(random-vega-lite-plot 9)

Cytoscape.js

(def cytoscape-example
  {:elements {:nodes [{:data {:id "a" :parent "b"} :position {:x 215 :y 85}}
                      {:data {:id "b"}}
                      {:data {:id "c" :parent "b"} :position {:x 300 :y 85}}
                      {:data {:id "d"} :position {:x 215 :y 175}}
                      {:data {:id "e"}}
                      {:data {:id "f" :parent "e"} :position {:x 300 :y 175}}]
              :edges [{:data {:id "ad" :source "a" :target "d"}}
                      {:data {:id "eb" :source "e" :target "b"}}]}
   :style [{:selector "node"
            :css {:content "data(id)"
                  :text-valign "center"
                  :text-halign "center"}}
           {:selector "parent"
            :css {:text-valign "top"
                  :text-halign "center"}}
           {:selector "edge"
            :css {:curve-style "bezier"
                  :target-arrow-shape "triangle"}}]
   :layout {:name "preset"
            :padding 5}})

(kind/cytoscape cytoscape-example)

(kind/cytoscape [cytoscape-example
                 {:style {:height 100
                          :width 100}}])

Apache Echarts

(kind/echarts
 {:xAxis {:data ["Mon" "Tue" "Wed" "Thu" "Fri" "Sat" "Sun"]}
  :yAxis {}
  :series [{:type "bar"
            :color ["#7F5F3F"]
            :data [23 24 18 25 27 28 25]}]})

MathBox.cljs

inspired by the official MathBox.cljs tutorial

(kind/hiccup
 '[(let [Data (fn []
                [mathbox.primitives/Interval
                 {:expr (fn [emit x _i t]
                          (emit x (Math/sin (+ x t))))
                  :width 64
                  :channels 2}])
         Curve (fn []
                 [:<>
                  [Data]
                  [mathbox.primitives/Line {:width 5
                                            :color "#3090FF"}]])
         Main (fn []
                [mathbox.core/MathBox
                 {:container {:style {:height "400px" :width "100%"}}
                  :focus 3}
                 [mathbox.primitives/Camera {:position [0 0 3]
                                             :proxy true}]
                 [mathbox.primitives/Cartesian
                  {:range [[-2 2] [-1 1]]
                   :scale [2 1]}
                  [mathbox.primitives/Axis {:axis 1 :width 3 :color "black"}]
                  [mathbox.primitives/Axis {:axis 2 :width 3 :color "black"}]
                  [mathbox.primitives/Grid {:width 2 :divideX 20 :divideY 10}]
                  [Curve]]])
         *state (r/atom {:open? false})]
     (fn []
       [:div
        [:button {:on-click #(swap! *state update :open? not)}
         (if (:open? @*state)
           "close"
           "open")]
        (when (:open? @*state)
          [Main])]))])

plotly

(kind/hiccup
 '[plotly
   {:data [{:x [0 1 3 2]
            :y [0 6 4 5]
            :z [0 8 9 7]
            :type :scatter3d
            :mode :lines+markers
            :opacity 0.5
            :line {:width 5}
            :marker {:size 4
                     :colorscale :Viridis}}]}])

Katex

(kind/hiccup
 '[katex "1+x^2"])

Emmy

(kind/hiccup
 '(require '[emmy.env :as e :refer [D]]))

(kind/hiccup
 [:div
  '(-> 'x
       ((D e/cube))
       e/simplify
       e/->infix)])

(kind/hiccup
 '[katex
   (-> 'x
       ((D e/cube))
       e/simplify
       e/->infix)])

tmdjs

(kind/hiccup
 '(require '[tech.v3.dataset :as tmd]))

(kind/hiccup
 '[(fn []
     [:div
      (-> {:x [1 2 3]}
          tmd/->dataset
          :x
          pr-str)])])

3dmol

(experimental)

(kind/hiccup
 ['three-d-mol-viewer
  {:data-pdb "2POR"}])

(kind/hiccup
 ['(fn [{:keys [pdb-data]}]
     [:div
      {:style {:width "100%"
               :height "500px"
               :position "relative"}
       :ref (fn [el]
              (let [config (clj->js
                            {:backgroundColor "0xffffff"})
                    viewer (.createViewer js/$3Dmol el #_config)]
                (.setViewStyle viewer (clj->js
                                       {:style "outline"}))
                (.addModelsAsFrames viewer pdb-data "pdb")
                (.addSphere viewer (clj->js
                                    {:center {:x 0
                                              :y 0
                                              :z 0}
                                     :radius 1
                                     :color "green"}))
                (.zoomTo viewer)
                (.render viewer)
                (.zoom viewer 0.8 2000)))}
      ;; need to keep this symbol to let Clay infer the necessary dependency
      'three-d-mol])
  {:pdb-data (memoized-slurp "https://files.rcsb.org/download/2POR.pdb")}])

Leaflet

(kind/hiccup
 ['(fn []
     [:div
      {:style {:width "100%"
               :height "500px"}
       :ref (fn [el]
              (let [m (-> js/L
                          (.map el)
                          (.setView (clj->js [52.5274319 13.4004289])
                                    19))]
                (-> js/L
                    (.tileLayer "https://tile.openstreetmap.org/{z}/{x}/{y}.png"
                                (clj->js {:maxZoom 19
                                          :attribution "© OpenStreetMap"}))
                    (.addTo m))))}
      'leaflet])])

Delays

Clojure Delays are a common way to define computations that do not take place immediately. The computation takes place when dereferencing the value for the first time. Clay makes sure to dererence Delays when passing values for visualization. This is handy for slow example snippets and explorations, that one would typically not like to slow down the evaluation of the whole namespace, but would like to visualize them on demand and also include in them in the final document.

(delay
  (Thread/sleep 500)
  (+ 1 2))

3

(delay
  [:div [:big "hi......."]])

[:div [:big "hi......."]]

Tests

clojure.test

Clay offers a few features supporting the use of standard Clojure tests.

(require '[clojure.test :refer [deftest is]]
         '[scicloj.kindly-default.v1.api :refer [is->]])

nil

Tests returning a boolean value (as they usually do, ending with a check) are rendered displaying that value as a clear x (failure) or v (success) mark:

(def test-dataset
  (tc/dataset {:x [1 2 3]
               :y [4 5 6]}))

(deftest mytest1
  (-> test-dataset
      tc/row-count
      (= 3)
      is))

Tests returning a non-boolean value are rendered simply displaying that value:

(deftest mytest2
  (-> test-dataset
      tc/row-count
      (= 3)
      is)
  test-dataset)

The is-> function allows performing a few checks in a pipeline and returning a different value to be displayed:

(deftest mytest3
  (-> 2
      (+ 3)
      (is-> > 4)
      (* 10)
      (is-> = 50)
      (* 10)))

500

These features open the way for literate testing / testable documentation solutions, such as those we have been using in the past (e.g., in tutorials of ClojisR using Notespace v2).